sortmerna (7.1.0-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.7.4 (routine-update) * Reflow Uploaders field (cme) * Remove Priority field (cme) * Set upstream metadata fields: Bug-Database, Repository-Browse. * debputy lint --auto-fix (routine-update) * Drop sse2-support dependency Closes: #1144278 * Set upstream metadata fields: Bug-Submit, Repository-Browse. * d/control: - add build-deps librapidarchive-dev, libparasail-dev, libbbhash-dev and zlib1g-dev - drop rapidjson-dev and libconcurrentqueue-dev. * add rapidarchive.patch: use system librapidarchive * add smr-api-disable.patch: skip the self-contained static bundle, which needs static parasail/rocksdb not available in Debian * d/copyright: drop the ssw.c stanza, SSW was removed upstream * d/man/sortmerna.1: update for the 7.1.0 command line * d/tests: rewrite the autopkgtest to run the binary end-to-end against the upstream tiny/small reference data (FASTA, SAM, BLAST and gzip input) and drop the "superficial" restriction. Closes: #1072346 * Build on big endian 64 architectures (upstream supports AMD64 and ARM64) * Drop the i386-only -msse2 workaround. i386 cannot be built anyway because libbbhash-dev is not available there. * d/rules: build with CMake directly instead of pybuild. Newer dh-python delegates to CMake, but older versions (as in trixie) run "setup.py clean", which the upstream setup.py does not implement, so the build failed on arm64. * d/tests: only copy the test data files that are actually needed. * d/salsa-ci.yml: - Do not build on i386 - Do not fail on blhc -- Andreas Tille Mon, 19 Oct 2026 21:47:24 +0200 sortmerna (4.3.7-3) unstable; urgency=medium * c23.patch: new: fix build failure with bool redefinition. (Closes: #1097910) * d/watch: port to v5 Github template. * d/control: declare compliance to standards version 4.7.2. * d/control: drop redundant Rules-Requires-Root: no. * concurrentqueue.h.patch: normalize Last-Update. * d/copyright: point to the versioned LGPL-3. -- Étienne Mollier Sun, 05 Oct 2025 23:01:51 +0200 sortmerna (4.3.7-2) unstable; urgency=medium * Fix Python3.12 string syntax Closes: #1087092 * d/copyright: Fixes thanks to lrc -- Andreas Tille Wed, 11 Dec 2024 17:38:13 +0100 sortmerna (4.3.7-1) unstable; urgency=medium * New upstream version 4.3.7 * cmake_RocksDB.patch: delete: patch now irrelevant. * rapidjson.patch: delete: patch now irrelevant. * no_static_linking.patch: delete: affected hunk disappeared upstream. * typos.patch: delete: affected hunks disappeared upstream. * d/{control,rules}: migrate to pybuild and dh-sequence-python3. * d/tests/: bring back superficial verifications. The way of using sortmerna changed over time, but the test suite proposed for autopkgtest needs involved adjustments. Most of the meat of the script is currently skipped, to only verify version and usage information can be shown to end users. Not ideal, but better than no tests at all. * d/{watch,u/metadata}: adjust to github redirection. * d/control: point the homepage to the github project. The original homepage on Université de Lille website does not look to be available anymore. * d/control: declare compliance to standards version 4.7.0. -- Étienne Mollier Sat, 01 Jun 2024 14:27:59 +0200 sortmerna (4.3.6-3) unstable; urgency=medium * d/rules: convert example files to Unicode per lintian flag. * typos.patch: add; fix typos caught by lintian. * d/copyright: update copyright year. * concurrentqueue.h.patch: update concurrentqueue.h location. (Closes: #1051325) * gcc-13.patch: new: fix ftbfs with gcc-13. -- Étienne Mollier Wed, 06 Sep 2023 19:43:10 +0200 sortmerna (4.3.6-2) unstable; urgency=medium * d/rules: remove dh_clean override; not needed anymore. * d/rules: move to execute_after_ statements. * d/rules: verbose remove of cmake/ directories. * d/rules: verbose permissions changes. * d/control: add myself to uploaders. * d/control: declare compliance to standards version 4.6.2. * d/rules: build for i386 with -msse2. The package depends on sse2-support for that architecture, so this is not a baseline violation in this particular case. (Closes: #1028122) -- Étienne Mollier Sat, 07 Jan 2023 16:52:43 +0100 sortmerna (4.3.6-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.6.1 (routine-update) -- Andreas Tille Tue, 29 Nov 2022 18:06:13 +0100 sortmerna (4.3.4-1) experimental; urgency=medium [ Steffen Möller ] * Update watch - we missed a couple of versions [ Andreas Tille ] * New upstream version * debhelper-compat 13 (routine-update) * Standards-Version: 4.6.0 (routine-update) * Build-Depends: cmake * Remove Tim Booth from Uploaders (thanks for all your work Tim) * Versioned Build-Depends: librocksdb-dev (>= 6.25.3) * Build-Depends: libgflags-dev, libsnappy-dev, libzstd-dev (needed by librocksdb-dev (>= 6.25.3) - see #1004665) * Build-Depends: rapidjson-dev, libconcurrentqueue-dev * Review copyright * Deactivate autopkgtest which is based on binary indexdb_rna which is not available any more * Use tags in watch file * Warn users about missing binary indexdb_rna in NEWS.Debian -- Andreas Tille Tue, 15 Feb 2022 19:51:10 +0100 sortmerna (2.1-5) unstable; urgency=medium * Team upload. [ Pranav Ballaney ] * Add autopkgtest template and README.test * Install examples * Add autopkgtests [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) -- Pranav Ballaney Sat, 21 Mar 2020 00:57:31 +0530 sortmerna (2.1-4) unstable; urgency=medium * Use 2to3 to port from Python2 to Python3 Closes: #945707 * debhelper-compat 12 * Standards-Version: 4.4.1 * Secure URI in copyright format * Use secure URI in Homepage field. * Set upstream metadata fields: Bug-Database, Bug-Submit (from ./configure), Repository, Repository-Browse. -- Andreas Tille Wed, 25 Dec 2019 21:25:41 +0100 sortmerna (2.1-3) unstable; urgency=medium [ Steffen Moeller ] * debian/upstream/metadata - added references to registries - yamllint cleanliness [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 -- Andreas Tille Tue, 09 Oct 2018 17:26:27 +0200 sortmerna (2.1-2) unstable; urgency=medium * Moved packaging from SVN to Git * debhelper 10 * Standards-Version: 4.1.0 (no changes needed) * Restrict set of architectures, Depends: sse2-support on i386 Closes: #818505 * hardening=+all -- Andreas Tille Mon, 25 Sep 2017 13:32:01 +0200 sortmerna (2.1-1) unstable; urgency=medium * New upstream version -- Andreas Tille Thu, 10 Mar 2016 23:39:18 +0100 sortmerna (2.0-1) unstable; urgency=medium * Initial upload to Debian (Closes: #794607) -- Andreas Tille Tue, 04 Aug 2015 21:27:07 +0200 sortmerna (2.0-0biolinux1) trusty; urgency=medium * Initial release. * Lose memcheck.h from the build to simplify licensing. -- Tim Booth Fri, 13 Feb 2015 18:00:35 +0000